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jobs crash for specific session (13sep27e) #2547

Open leginonbot opened 3 months ago

leginonbot commented 3 months ago

Author Name: Gira Bhabha (Gira Bhabha) Original Redmine Issue: 2547, https://emg.nysbc.org/redmine/issues/2547 Original Date: 2013-10-04 Original Assignee: Gira Bhabha

ctffind and dogpicker jobs crash for session 13sep27e, with the following error.

AttributeError: 'module' object has no attribute 'MoverParamsData'

jobs end within a few seconds (on goby & guppy)

details:

[gbhabha@goby ~]$ /opt/myamisnap/bin/appion dogPicker.py --projectid=382 --preset=en --session=13sep27e --runname=dogrun1 --rundir=/ami/exdata/appion/13sep27e/extract/dogrun1 --no-rejects --no-wait --commit --continue --peaktype=centerofmass --maxthresh=1.5 --thresh=0.5 --median=2 --lowpass=15 --highpass=0 --planereg --bin=4 --diam=140 --pixlimit=4.0 --kfactor=1.5 --expid=12404 --jobtype=dogpicker

... Time stamp: 13oct04l33 ... Function name: dogPicker ... Appion directory: /opt/myamisnap/lib ... Using split database Connected to database: 'ap382' ... Committing data to database !!! WARNING: lowpass filter value greater than zero; will ignore ... Found project id=382 for session 13sep27e in 5.64 msec ... Run directory: /ami/exdata/appion/13sep27e/extract/dogrun1 !!! WARNING: directory '/ami/exdata/appion/13sep27e/extract/dogrun1' already exists. ... Writing function log to: dogPicker.log ... Running on host: goby.amigroup.scripps.edu ... Uploading ScriptData.... ... Running on host: goby.amigroup.scripps.edu ... Found 16 processors on this machine !!! WARNING: More than one cluster job has this path ... Running Appion version 'trunk' ... Reading old done dictionary: dogPicker.donedict ... Found 1 done dictionary entries ... Querying database for preset 'en' images from session '13sep27e' ...

Traceback (most recent call last): File "/opt/myamisnap/bin/dogPicker.py", line 78, in imgLoop.run() File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 65, in run self._getAllImages() File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 486, in _getAllImages self.imgtree = apDatabase.getImagesFromDB(self.params['sessionname'], self.params['preset']) File "/opt/myamisnap/lib/appionlib/apDatabase.py", line 83, in getImagesFromDB imgtree = imgquery.query(readimages=False) File "/opt/myamisnap/lib/sinedon/data.py", line 395, in query results = db.query(self, *kwargs) File "/opt/myamisnap/lib/sinedon/dbdatakeeper.py", line 95, in query result = self._query(args, **kwargs) File "/opt/myamisnap/lib/sinedon/dbdatakeeper.py", line 118, in _query myresult = result.fetchall() File "/opt/myamisnap/lib/sinedon/sqldict.py", line 577, in fetchall cursorresult = self._format(subfetch, qikey) File "/opt/myamisnap/lib/sinedon/sqldict.py", line 650, in _format result = map(sql2data, sqlresult, qikeylist, qinfolist) File "/opt/myamisnap/lib/sinedon/sqldict.py", line 1282, in sql2data content = datatype(in_dict, join=join, parentclass=parentclass) File "/opt/myamisnap/lib/sinedon/sqldict.py", line 1372, in datatype dclass = findDataClass(modulename, dclassname) File "/opt/myamisnap/lib/sinedon/sqldict.py", line 1308, in findDataClass cls = getattr(mod, classname) AttributeError: 'module' object has no attribute 'MoverParamsData'

leginonbot commented 3 months ago

Original Redmine Comment Author Name: Sargis Dallakyan (@dallakyan) Original Date: 2013-10-09T17:10:20Z

MoverParamsData seems to be a new table in dbemdata. I don't know what it is used for; couldn't find any reference to it. Maybe this needs an entry in leginon/leginondata.py for it to work.

leginonbot commented 3 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2013-10-09T18:57:16Z

Just checked,

On guppy head node, /opt/myamisnap/lib/leginon/leginondata.py does have MoverParamsData Also good on guppy-29. I was able to run dogpicker of my session o.k.

I don't have goby account, but asked Jeff to check for me on goby Neighther the headnode nor one of the node we got on with qsub -I has MoverParamsData.

MoverParamsData was added in r17925, dated on Monday. Maybe goby is not up to date?

leginonbot commented 3 months ago

Original Redmine Comment Author Name: Sargis Dallakyan (@dallakyan) Original Date: 2013-10-10T14:24:41Z

Thanks Anchi. I have copied /opt/myamisnap from guppy to goby and I see MoverParamsData in /opt/myamisnap/lib/leginon/leginondata.py now.

Gira, please try again and change the status of this bug report to closed if it works for you. Thanks.